You'll find documentation for all the augur subcommands below.
We're in the process of adding examples and more extensive documentation for each command, but at a minimum each subcommand will contain autogenerated documentation similar to that seen by running --help.
.. toctree::
:maxdepth: 1
parse
curate/index
merge
index
filter
mask
align
tree
refine
ancestral
translate
reconstruct-sequences
clades
traits
sequence-traits
lbi
distance
titers
frequencies
export
validate
version
import
measurements
read-file
write-file